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Command:
jip run --dry MethRep.jip -i test_files/all.mult_diff.map -r test_files/rmsk.clean.bed -b TEST ####################################################################################### | Pipeline Configuration | +--------------------------------+----------------------------------------------------+ | Name | Value | +================================+====================================================+ | input | test_files/all.mult_diff.map | | repBed | test_files/rmsk.clean.bed | | base | TEST | | p | False | +--------------------------------+----------------------------------------------------+ ####################################################################################### | Job - FilterMapping | +--------------------------------+----------------------------------------------------+ | Name | Value | +================================+====================================================+ | input | test_files/all.mult_diff.map | | base | TEST | | p | False | | unique | TEST.unique.map | | multi | TEST.mult.map | | uniqOEA | TEST.uniq_OEA.map | | multOEA | TEST.mult_OEA.map | | multD | TEST.mult_diff.map | +--------------------------------+----------------------------------------------------+ ####################################################################################### | Job - TEST | +--------------------------------+----------------------------------------------------+ | Name | Value | +================================+====================================================+ | input | [u'TEST.mult.map', u'TEST.unique.map', | | | u'TEST.mult_OEA.map'] | | cmd | [u'echo TEST.unique.map'] | | outfile | | | output | <<STREAM>> | +--------------------------------+----------------------------------------------------+ ####################################################################################### | Job - TEST.1 | +--------------------------------+----------------------------------------------------+ | Name | Value | +================================+====================================================+ | input | [u'TEST.mult.map', u'TEST.unique.map', | | | u'TEST.mult_OEA.map'] | | cmd | [u'echo TEST.mult.map'] | | outfile | | | output | <<STREAM>> | +--------------------------------+----------------------------------------------------+ ####################################################################################### | Job - TEST.2 | +--------------------------------+----------------------------------------------------+ | Name | Value | +================================+====================================================+ | input | [u'TEST.mult.map', u'TEST.unique.map', | | | u'TEST.mult_OEA.map'] | | cmd | [u'echo TEST.mult_OEA.map'] | | outfile | | | output | <<STREAM>> | +--------------------------------+----------------------------------------------------+ ##################################################################################################################################################### | Job states | +--------------------------------+--------+----------------------------------------------------+----------------------------------------------------+ | Name | State | Inputs | Outputs | +================================+========+====================================================+====================================================+ | FilterMapping | Hold | test_files/all.mult_diff.map | TEST.unique.map, TEST.mult.map, TEST.uniq_OEA.map, | | | | | TEST.mult_OEA.map, TEST.mult_diff.map | | TEST | Hold | TEST.mult.map, TEST.unique.map, TEST.mult_OEA.map | | | TEST.1 | Hold | TEST.mult.map, TEST.unique.map, TEST.mult_OEA.map | | | TEST.2 | Hold | TEST.mult.map, TEST.unique.map, TEST.mult_OEA.map | | +--------------------------------+--------+----------------------------------------------------+----------------------------------------------------+ ##################### | Job hierarchy | ##################### FilterMapping (MethRep) ├─TEST ├─TEST.1 └─TEST.2 ##################### | Tasks: 4 | | Jobs: 4 | | Named Groups: 1 | | Job Groups: 1 | #####################
Files used:
FilterMap.jip:
#!/usr/bin/env jip # Split map files by their mappings # # Usage: # FilterMap.jip -i <MapFile> [-b <prefix_output>] [-p] # # Inputs: # -i, --input <MapFilet> MAP file # # Options: # -b, --base <prefix_output> Prefix name output [default: out] # -p Data is paired-end # # # #%begin init add_output('unique', '${base}.unique.map') add_output('multi', '${base}.mult.map') add_output('uniqOEA', '${base}.uniq_OEA.map') add_output('multOEA', '${base}.mult_OEA.map') add_output('multD', '${base}.mult_diff.map') #%end echo "${input}" python filter_map.py -i ${input} -o ${base} ${p|arg("-p")}
MethRep.jip: #! /usr/bin/env jip # #Locate reads that map in repetitive regions # #Usage: # MetRep.jip -i -r <rmsk.bed> -b <prefix_output> [-p] # #Inputs: # -i, --input Mapping file from gem # -r, --repBed <rmsk.bed> Repetitive regions in BED format # # #Options: # -b, --base <prefix_output> Prefix output # -p Flag if mapping is paired #
#%begin pipeline sepMap = job('FilterMapping').run("FilterMap", input=opts["input"], base=base, p=p) f = job("${base}").bash("echo ${input}", input=[sepMap.unique, sepMap.multi, sepMap.multOEA]) #%end
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Command:
Files used:
FilterMap.jip:
MethRep.jip:
#! /usr/bin/env jip
#
#Locate reads that map in repetitive regions
#
#Usage:
# MetRep.jip -i -r <rmsk.bed> -b <prefix_output> [-p]
#
#Inputs:
# -i, --input Mapping file from gem
# -r, --repBed <rmsk.bed> Repetitive regions in BED format
#
#
#Options:
# -b, --base <prefix_output> Prefix output
# -p Flag if mapping is paired
#
The text was updated successfully, but these errors were encountered: